@Duncan
There are as many protocols as there are users; I found $0.02 so here is what I do.
First off, because you have a WD HDD, go
here and DL the free WD version of Acronis True Image, an excellent imaging app. On HDD 0, create a small, OS-only primary partition. How small is small? I have a 100GB OS partition on which I have 250+ apps presently occupying 62GB of space. You be the judge for your anticipated needs. On that partition place ONLY the OS and everyday apps (e.g., utilities, browser, flash, Office, etc.). On the same HDD, create two more primary partitions, one for such things as MP3s, JPEGs, docs. The third partition you are going to use for storing image backups from HDD 1, but more on that later.
Do the same thing with the second HDD: create three primary partitions, two for stuff (maybe you divide your MP3s, docs, etc, between the two HDDs) one for games, and the third for image backups from HDD 0. Now if you want more than three partitions on the HDDs you will have to create logical/extended partitions.
Now the rationale. More than anyplace else, it is your OS partition that is going to become corrupt by malware, patches, tweaks, SW removal (of shared files), etc. Therefore, it is good practice to regularly and frequently create image backups of your OS partition. Do this religiously. Many people are content to place the image backups on the same HDD that is being backed up. That is fine - unless your HDD bricks upon which you will not only lose your OS but you will also lose your backups. Therefore, you place ALL (not just your OS) of your backups of HDD 0 on HDD 1. Why? The odds of both HDDs bricking at the same time is nil. Now, of course, 15 people will post telling you of the time when all of the HDDs in their machines went up in flames simultaneously. That ain't going to happen but I have you covered for that just in case. Later.
The small OS partition facilitates fast image backup creation. Mine take about 16 minutes. If you are regularly backing up a 3, 4, 500GB partition, you will doze off while waiting for it to complete. Secondly, this week, e.g., maybe you did not add any MP3s to your collection: why back those up again? In other words, if most of your stuff is on one or two large partitions, you are backing up everything again and again whether it needs to be or not. (I will defer discussions about incremental or differential backups). Therefore, you only have to back up the remaining partitions when changes to them are made. By dividing your data over two HDDs, that data is able to reside in small partitions. For example, as I have explained so far, you have six partitions: two contain saved image backups, one contains the OS, and the other three can be divided any way you like. And if you desire, as I said, you can create additional logical/extended partitions on each drive.
This protocol gives you two sets of complete data from each HDD on separate HDDs: you working copies and your image backups. To carry safety one step further, it is best to store crucial data on some external device. I do not do that for all of my data (because the odds of my entire machine going up in flames is nil, as I said. But I do store data that I think is extraordinary critical on USB flash drives; some people like external HDDs. I do not have the need to superprotect much data so a 30GB flash drive is fine for me. Besides, I have 3, 750GB internal HDDs and simply do not need any more storage space.
One more thing: unless you are a gambler, do not store critical data on optical media - because it degrades in time. You can always transfer data to new discs but apart from the nuisance, you may suffer read-write errors even though your burning app verified the integrity of the burn.
Gee, that all looks like $0.04 worth.
Monk